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Sca1+ Progenitor Cells (Ex vivo) Exhibits Differential Proteomic Signatures From the Culture Adapted Sca1+ Cells (In vitro), Both Isolated From Murine Skeletal Muscle Tissue

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Abstract

Stem cell antigen-1 (Sca-1) is a glycosyl-phosphatidylinositol-anchored membrane protein that is expressed in a sub-population of muscle stem and progenitor cell types. Reportedly, Sca-1 regulates the myogenic property of myoblasts and Sca-1−/− mice exhibited defective muscle regeneration. Although the role of Sca-1 in muscle development and maintenance is well-acknowledged, molecular composition of muscle derived Sca-1+ cells is not characterized. Here, we applied a high-resolution mass spectrometry-based workflow to characterize the proteomic landscape of mouse hindlimb skeletal muscle derived Sca-1+ cells. Furthermore, we characterized the impact of the cellular microenvironments on the proteomes of Sca-1+ cells. The proteome component of freshly isolated Sca-1+ cells (ex vivo) was compared with that of Sca-1+ cells expanded in cell culture (in vitro). The analysis revealed significant differences in the protein abundances in the two conditions reflective of their functional variations. The identified proteins were enriched in various biological pathways. Notably, we identified proteins related to myotube differentiation, myotube cell development and myoblast fusion. We also identified a panel of cell surface marker proteins that can be leveraged in future to enrich Sca-1+ cells using combinatorial strategies. Comparative analysis implicated the activation of various pathways leading to increased protein synthesis under in vitro condition. We report here the most comprehensive proteome map of Sca-1+ cells that provides insights into the molecular networks operative in Sca-1+ cells. Importantly, through our work we generated the proteomic blueprint of protein abundances significantly altered in Sca-1+ cells under ex vivo and in vitro conditions. The curated data can also be visualized at https://yenepoya.res.in/database/Sca-1-Proteomics.

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Data Availability

The MS raw files (.raw) and Proteome Discoverer search files(.msf) are available at http://www.ebi.ac.uk/pride/archive/ with the PRIDE dataset identifier PXD022247. The curated data can also be visualized at https://yenepoya.res.in/database/Sca-1-Proteomics.

Code Availability

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Acknowledgements

The authors would like to acknowledge the MASSFIITB Facility at IIT Bombay supported by the Department of Biotechnology (BT/PR13114/INF/22/206/2015) to carry out all MS-related experiments.

Funding

The authors would like to thank the Stem Cells and Regenerative Medicine Centre of Yenepoya Research Centre, Yenepoya (Deemed to be University) for providing the infrastructure, core facility and funding in the form of Yenepoya University Seed Grant (YU/Seed Grant/2015-042) awarded to the Principal Investigator Dr Bipasha Bose to carry out this study.

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Authors and Affiliations

  1. Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, Karnataka, 575018, India

    Saketh Kapoor, Sudheer Shenoy P & Bipasha Bose

  2. Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, Karnataka, 575018, India

    Pratigya Subba

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  1. Saketh Kapoor
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Contributions

BB, SK and SS conceived and designed the study. SK and SS performed the animal experiments. SK carried out the MS sample preparation, analysed and performed the data analysis. SK and PS wrote the manuscript. BB and SS edited and approved the manuscript.

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Correspondence to Sudheer Shenoy P or Bipasha Bose.

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This study was approved by the Institutional Animal Ethics Committee, Yenepoya (Deemed to be University) bearing number 10/4.8.2015. 

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Supplementary Information

Table S1

The entire list of proteins identified in the Sca-1+ex vivo and in vitro conditions (XLSX 424 kb)

Table S2

List of regulatory proteins identified in this study. (XLSX 20 kb)

Table S3

List of proteins which are differentially expressed between Sca-1+ex vivo and in vitro condition (XLSX 377 kb)

Fig. S1

Morphology of Sca-1+ sorted cells after 72 h of culturing (PNG 1427 kb)

High Resolution Image (TIF 924 kb)

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Kapoor, S., Subba, P., Shenoy P, S. et al. Sca1+ Progenitor Cells (Ex vivo) Exhibits Differential Proteomic Signatures From the Culture Adapted Sca1+ Cells (In vitro), Both Isolated From Murine Skeletal Muscle Tissue. Stem Cell Rev and Rep 17, 1754–1767 (2021). https://doi.org/10.1007/s12015-021-10134-w

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